sourmash

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BIOM format would enable direct import as a phyloseq object (ref #2156) and is a standard format folks can use downstream. BIOM version 2.1 spec: https://biom-format.org/documentation/format_versions/biom-2.1.html early examples seem really...

bluegenes

support distance matrix output from `compare`?

1

`sourmash compare` outputs a similarity matrix. Many tools want the opposite, a distance matrix. It would be relatively straightforward to support `--distance` (outputs 1-value). This would work for jaccard, containment,...

bluegenes

`sourmash tax genome` may fail silently with `--force` and incorrect gather inputs

1

`sourmash tax genome --force` fails silently or yields confusing error if you pass in multiple gather results for the same query I accidentally passed in both k7 and k10 gather...

bluegenes

zipfile databases could include taxonomy information

7

I think I mentioned this as part of another issue, but I think it would make taxonomy analyses a bit simpler if we included our taxonomy csv (optionally formatted as...

bluegenes

document containment direction for `compare` (and standardize for containment ani)

1

When running `sourmash compare`, the matrix will be asymmetric. But which direction is which? And is it the same for `containment` and `containment-ani`? Based on code here: https://github.com/sourmash-bio/sourmash/blob/latest/src/sourmash/compare.py#L75-L90 For `--containment`,...

bluegenes

Bump thiserror from 1.0.31 to 1.0.32

1

Bumps [thiserror](https://github.com/dtolnay/thiserror) from 1.0.31 to 1.0.32. Release notes Sourced from thiserror's releases. 1.0.32 Add keywords to crates.io metadata Commits 8cb98af Release 1.0.32 c1fb583 Disable nightly backtrace testing until converted to...

dependabot[bot]

Bump serde_json from 1.0.82 to 1.0.83

1

Bumps [serde_json](https://github.com/serde-rs/json) from 1.0.82 to 1.0.83. Release notes Sourced from serde_json's releases. v1.0.83 Add categories to crates.io metadata Commits 2b0403f Release 1.0.83 db96d72 Add categories to crates.io metadata 2512933 Add...

dependabot[bot]

Bump ouroboros from 0.15.0 to 0.15.2

1

Bumps [ouroboros](https://github.com/joshua-maros/ouroboros) from 0.15.0 to 0.15.2. Commits See full diff in compare view [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) You can trigger a rebase of this PR by commenting `@dependabot rebase`. [//]: #...

dependabot[bot]

better handle taxonomic identifiers from RefSeq/Genbank

3

I'm having trouble matching some of my protein sigs to the rs207 taxonomy, and I'm noticing some mismatches in `GCA` vs `GCF` identifiers. Looking at a taxonomy csv ``` grep...

bluegenes

prepared databases may be incorrect/corrupted?

10

Hi, When I run `sourmash gather` as follows, I get the above error message: ``` $ sourmash gather --ksize 51 --dna ../dat/query/query.sig ../dat/db/k51/genbank-2022.03-bacteria-k51.zip -o results_test.txt == This is sourmash version...

aboffin